51
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Javed Z, Nguyen HH, Harker K, Mohr CM, Vano P, Wallace SR, Silvers C, Sim C, Turumella S, Flinn A, Carter-O’Connell I. Identification of a Novel PARP14 Site Motif and Glycohydrolase Specificity Using TLC-MALDI-TOF. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533863. [PMID: 36993563 PMCID: PMC10055325 DOI: 10.1101/2023.03.22.533863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) to target proteins is mediated by a class of human poly-ADP-ribose polymerases, PARPs, and removal of ADPr is catalyzed by a family of glycohydrolases. Although thousands of potential ADPr modification sites have been identified using high-throughput mass-spectrometry, relatively little is known about sequence specificity encoded near the modification site. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates the discovery and validation of ADPr site motifs. We identify a minimal 5-mer peptide sequence that is sufficient to drive PARP14 specific activity while highlighting the importance of the adjacent residues in PARP14 targeting. We measure the stability of the resultant ester bond and show that non-enzymatic removal is sequence independent and occurs within hours. Finally, we use the ADPr-peptide to highlight differential activities within the glycohydrolase family and their sequence specificities. Our results highlight: 1) the utility of MALDI-TOF in motif discovery and 2) the importance of peptide sequence in governing ADPr transfer and removal.
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Affiliation(s)
- Zeeshan Javed
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Hannah H. Nguyen
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Kiana Harker
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Christian M. Mohr
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Pia Vano
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Sean R. Wallace
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Clarissa Silvers
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Colin Sim
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Soumya Turumella
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Ally Flinn
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
| | - Ian Carter-O’Connell
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California, 95053, United States
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52
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IFN-Induced PARPs—Sensors of Foreign Nucleic Acids? Pathogens 2023; 12:pathogens12030457. [PMID: 36986379 PMCID: PMC10057411 DOI: 10.3390/pathogens12030457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Cells have developed different strategies to cope with viral infections. Key to initiating a defense response against viruses is the ability to distinguish foreign molecules from their own. One central mechanism is the perception of foreign nucleic acids by host proteins which, in turn, initiate an efficient immune response. Nucleic acid sensing pattern recognition receptors have evolved, each targeting specific features to discriminate viral from host RNA. These are complemented by several RNA-binding proteins that assist in sensing of foreign RNAs. There is increasing evidence that the interferon-inducible ADP-ribosyltransferases (ARTs; PARP9—PARP15) contribute to immune defense and attenuation of viruses. However, their activation, subsequent targets, and precise mechanisms of interference with viruses and their propagation are still largely unknown. Best known for its antiviral activities and its role as RNA sensor is PARP13. In addition, PARP9 has been recently described as sensor for viral RNA. Here we will discuss recent findings suggesting that some PARPs function in antiviral innate immunity. We expand on these findings and integrate this information into a concept that outlines how the different PARPs might function as sensors of foreign RNA. We speculate about possible consequences of RNA binding with regard to the catalytic activities of PARPs, substrate specificity and signaling, which together result in antiviral activities.
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53
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Dhoonmoon A, Nicolae CM. Mono-ADP-ribosylation by PARP10 and PARP14 in genome stability. NAR Cancer 2023; 5:zcad009. [PMID: 36814782 PMCID: PMC9940457 DOI: 10.1093/narcan/zcad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
ADP-ribosylation is a post-translational modification involved in a variety of processes including DNA damage repair, transcriptional regulation, and cellular proliferation. Depending on the number of ADP moieties transferred to target proteins, ADP-ribosylation can be classified either as mono-ADP-ribosylation (MARylation) or poly-ADP-ribosylation (PARylation). This post-translational modification is catalyzed by enzymes known as ADP-ribosyltransferases (ARTs), which include the poly (ADP-ribose)-polymerase (PARP) superfamily of proteins. Certain members of the PARP family including PARP1 and PARP2 have been extensively studied and assessed as therapeutic targets. However, the other members of the PARP family of protein are not as well studied but have gained attention in recent years given findings suggesting their roles in an increasing number of cellular processes. Among these other members are PARP10 and PARP14, which have gradually emerged as key players in maintenance of genomic stability and carcinogenesis. PARP10 and PARP14 catalyze the transfer of a single ADP moiety to target proteins. Here, we summarize the current knowledge on MARylation in DNA repair and cancer, focusing on PARP10 and PARP14. We highlight the roles of PARP10 and PARP14 in cancer progression and response to chemotherapeutics and briefly discuss currently known PARP10 and PARP14 inhibitors.
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Affiliation(s)
- Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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54
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Mono-ADP-ribosylation by PARP10 inhibits Chikungunya virus nsP2 proteolytic activity and viral replication. Cell Mol Life Sci 2023; 80:72. [PMID: 36840772 PMCID: PMC9959937 DOI: 10.1007/s00018-023-04717-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Replication of viruses requires interaction with host cell factors and repression of innate immunity. Recent findings suggest that a subset of intracellular mono-ADP-ribosylating PARPs, which are induced by type I interferons, possess antiviral activity. Moreover, certain RNA viruses, including Chikungunya virus (CHIKV), encode mono-ADP-ribosylhydrolases. Together, this suggests a role for mono-ADP-ribosylation (MARylation) in host-virus conflicts, but the relevant substrates have not been identified. We addressed which PARP restricts CHIKV replication and identified PARP10 and PARP12. For PARP10, this restriction was dependent on catalytic activity. Replication requires processing of the non-structural polyprotein nsP1-4 by the protease located in nsP2 and the assembly of the four individual nsP1-nsP4 into a functional replication complex. PARP10 and PARP12 inhibited the production of nsP3, indicating a defect in polyprotein processing. The nsP3 protein encodes a macrodomain with de-MARylation activity, which is essential for replication. In support for MARylation affecting polyprotein processing, de-MARylation defective CHIKV replicons revealed reduced production of nsP2 and nsP3. We hypothesized that MARylation regulates the proteolytic function of nsP2. Indeed, we found that nsP2 is MARylated by PARP10 and, as a consequence, its proteolytic activity was inhibited. NsP3-dependent de-MARylation reactivated the protease. Hence, we propose that PARP10-mediated MARylation prevents polyprotein processing and consequently virus replication. Together, our findings provide a mechanistic explanation for the role of the viral MAR hydrolase in CHIKV replication.
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55
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Zielinska Z, Oldak L, Kacperczyk-Bartnik J, Koc-Żórawska E, Żórawski M, Laudanski P, Gorodkiewicz E. An Array SPRi Biosensor for the Determination on PARP-1 in Blood Plasma. Biomedicines 2023; 11:biomedicines11020602. [PMID: 36831138 PMCID: PMC9953221 DOI: 10.3390/biomedicines11020602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
A biosensor was developed for the quantification of poly(ADP-ribose) polymerase-1 (PARP-1) in body fluids. An antibody specific for PARP-1 was placed on a chip with cysteamine (linker) and a gold layer. This biosensor has a linear response range (10-1000 pg∙mL-1) under appropriate pH conditions and with an antibody ligand concentration of 5 ng∙mL-1. Plasma samples were diluted with PBS buffer in appropriate quantities so that they fell within the linear range of the calibration curve. The biosensor exhibited suitable precision and accuracy, and good recovery (at levels from 95% to 105%). The method was validated by means of PARP-1 determinations in plasma samples from patients with endometriosis and a control group, using surface plasmon resonance imaging (SPRi) biosensors and an enzyme-linked immunosorbent assay (ELISA) test. The Spearman correlation coefficient was close to 1. PARP-1 may be a marker providing information about pathological changes in the body during endometriosis.
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Affiliation(s)
- Zuzanna Zielinska
- Doctoral School of Exact and Natural Science, Faculty of Chemistry, University of Bialystok, 15-245 Bialystok, Poland
- Correspondence: (Z.Z.); (L.O.)
| | - Lukasz Oldak
- Doctoral School of Exact and Natural Science, Faculty of Chemistry, University of Bialystok, 15-245 Bialystok, Poland
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, 15-245 Bialystok, Poland
- Correspondence: (Z.Z.); (L.O.)
| | - Joanna Kacperczyk-Bartnik
- 2nd Department of Obstetrics and Gynecology, Medical University of Warsaw, 02-091 Warsaw, Poland
- Club 35, Polish Society of Gynecologists and Obstetricians, 53-125 Wrocław, Poland
| | - Ewa Koc-Żórawska
- II Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Bialystok, 15-276 Białystok, Poland
| | - Marcin Żórawski
- II Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Bialystok, 15-276 Białystok, Poland
| | - Piotr Laudanski
- OVIklinika Infertility Center, 01-377 Warsaw, Poland
- Women’s Health Research Institute, Calisia University, 62-800 Kalisz, Poland
- Department of Obstetrics, Gynaecology, Gynecology and Gynaecological Oncology, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Ewa Gorodkiewicz
- Bioanalysis Laboratory, Faculty of Chemistry, University of Bialystok, 15-245 Bialystok, Poland
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56
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The regulation loop of MARVELD1 interacting with PARP1 in DNA damage response maintains genome stability and promotes therapy resistance of cancer cells. Cell Death Differ 2023; 30:922-937. [PMID: 36750717 PMCID: PMC10070477 DOI: 10.1038/s41418-023-01118-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/28/2022] [Accepted: 12/13/2022] [Indexed: 02/09/2023] Open
Abstract
The DNA damage response (DDR) plays crucial roles in cancer prevention and therapy. Poly(ADP-ribose) polymerase 1 (PARP1) mediates multiple signal transduction in the DDR as a master regulator. Uncovering the regulatory factors of PARP1 contributes to a more comprehensive view of tumorigenesis and treatment strategies. Here, we reveal that MARVELD1 acts as a mediator of DDR to perform early events and maintain genome stability. Mechanistically, PARP1 PARylates MARVELD1 at D102, D118 and D130, and in turn, MARVELD1 stabilizes PARP1 by enhancing NAA50-mediated acetylation, thus forming a positive feedback loop. MARVELD1 knockout mice and their embryo fibroblasts exhibit genomic instability and shorter half-life of PARP1. Moreover, MARVELD1 partnering with PARP1 facilitates resistance to genotoxic drugs and disrupts PARP inhibitor (PARPi) effect in PDX model of colorectal cancer (CRC). Overall, our results underline the link between MARVELD1 and PARP1 in therapeutic resistance based on DDR and provide new insights for clinical tumor therapy of PARPi.
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57
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The DarT/DarG Toxin-Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies. Pathogens 2023; 12:pathogens12020240. [PMID: 36839512 PMCID: PMC9967889 DOI: 10.3390/pathogens12020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The chemical modification of cellular macromolecules by the transfer of ADP-ribose unit(s), known as ADP-ribosylation, is an ancient homeostatic and stress response control system. Highly conserved across the evolution, ADP-ribosyltransferases and ADP-ribosylhydrolases control ADP-ribosylation signalling and cellular responses. In addition to proteins, both prokaryotic and eukaryotic transferases can covalently link ADP-ribosylation to different conformations of nucleic acids, thus highlighting the evolutionary conservation of archaic stress response mechanisms. Here, we report several structural and functional aspects of DNA ADP-ribosylation modification controlled by the prototype DarT and DarG pair, which show ADP-ribosyltransferase and hydrolase activity, respectively. DarT/DarG is a toxin-antitoxin system conserved in many bacterial pathogens, for example in Mycobacterium tuberculosis, which regulates two clinically important processes for human health, namely, growth control and the anti-phage response. The chemical modulation of the DarT/DarG system by selective inhibitors may thus represent an exciting strategy to tackle resistance to current antimicrobial therapies.
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58
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Murthy S, Nizi MG, Maksimainen MM, Massari S, Alaviuhkola J, Lippok BE, Vagaggini C, Sowa ST, Galera-Prat A, Ashok Y, Venkannagari H, Prunskaite-Hyyryläinen R, Dreassi E, Lüscher B, Korn P, Tabarrini O, Lehtiö L. [1,2,4]Triazolo[3,4- b]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes. J Med Chem 2023; 66:1301-1320. [PMID: 36598465 PMCID: PMC9884089 DOI: 10.1021/acs.jmedchem.2c01460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report [1,2,4]triazolo[3,4-b]benzothiazole (TBT) as a new inhibitor scaffold, which competes with nicotinamide in the binding pocket of human poly- and mono-ADP-ribosylating enzymes. The binding mode was studied through analogues and cocrystal structures with TNKS2, PARP2, PARP14, and PARP15. Based on the substitution pattern, we were able to identify 3-amino derivatives 21 (OUL243) and 27 (OUL232) as inhibitors of mono-ARTs PARP7, PARP10, PARP11, PARP12, PARP14, and PARP15 at nM potencies, with 27 being the most potent PARP10 inhibitor described to date (IC50 of 7.8 nM) and the first PARP12 inhibitor ever reported. On the contrary, hydroxy derivative 16 (OUL245) inhibits poly-ARTs with a selectivity toward PARP2. The scaffold does not possess inherent cell toxicity, and the inhibitors can enter cells and engage with the target protein. This, together with favorable ADME properties, demonstrates the potential of TBT scaffold for future drug development efforts toward selective inhibitors against specific enzymes.
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Affiliation(s)
- Sudarshan Murthy
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Maria Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Serena Massari
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Juho Alaviuhkola
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Barbara E. Lippok
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Chiara Vagaggini
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Sven T. Sowa
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Albert Galera-Prat
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Yashwanth Ashok
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Harikanth Venkannagari
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | | | - Elena Dreassi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Bernhard Lüscher
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Patricia Korn
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy,
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland,
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Rack JGM, Ahel I. A Simple Method to Study ADP-Ribosylation Reversal: From Function to Drug Discovery. Methods Mol Biol 2023; 2609:111-132. [PMID: 36515833 DOI: 10.1007/978-1-0716-2891-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
ADP-ribosylation is an ancient modification of proteins, nucleic acids, and other biomolecules found in all kingdoms of life as well as in certain viruses. The regulation of fundamental (patho)physiological processes by ADP-ribosylation, including the cellular stress response, inflammation, and immune response to bacterial and viral pathogens, has created a strong interest into the study of modification establishment and removal to explore novel therapeutic approaches. Beyond ADP-ribosylation in humans, direct targeting of factors that alter host ADP-ribosylation signaling (e.g., viral macrodomains) or utilize ADP-ribosylation to manipulate host cell behavior (e.g., bacterial toxins) were shown to reduce virulence and disease severity. However, the realization of these therapeutic potentials is thus far hampered by the unavailability of simple, high-throughput methods to study the modification "writers" and "erasers" and screen for novel inhibitors.Here, we describe a scalable method for the measurement of (ADP-ribosyl)hydrolase activity. The assay relies on the conversion of ADP-ribose released from a modified substrate by the (ADP-ribosyl)hydrolase under investigation into AMP by the phosphodiesterase NudT5 into bioluminescence via a commercially available detection assay. Moreover, this method can be utilized to study the role of nudix- or ENPP-type phosphodiesterases in ADP-ribosylation processing and may also be adapted to investigate the activity of (ADP-ribosyl)transferases. Overall, this method is applicable for both basic biochemical characterization and screening of large drug libraries; hence, it is highly adaptable to diverse project needs.
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Affiliation(s)
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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60
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Epigenetic Insights on PARP-1 Activity in Cancer Therapy. Cancers (Basel) 2022; 15:cancers15010006. [PMID: 36612003 PMCID: PMC9817704 DOI: 10.3390/cancers15010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
The regulation of chromatin state and histone protein eviction have been proven essential during transcription and DNA repair. Poly(ADP-ribose) (PAR) polymerase 1 (PARP-1) and poly(ADP-ribosyl)ation (PARylation) are crucial mediators of these processes by affecting DNA/histone epigenetic events. DNA methylation/hydroxymethylation patterns and histone modifications are established by mutual coordination between all epigenetic modifiers. This review will focus on histones and DNA/histone epigenetic machinery that are direct targets of PARP-1 activity by covalent and non-covalent PARylation. The effects of these modifications on the activity/recruitment of epigenetic enzymes at DNA damage sites or gene regulatory regions will be outlined. Furthermore, based on the achievements made to the present, we will discuss the potential application of epigenetic-based therapy as a novel strategy for boosting the success of PARP inhibitors, improving cell sensitivity or overcoming drug resistance.
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61
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Immunoprecipitation Using Mono-ADP-Ribosylation-Specific Antibodies. Methods Mol Biol 2022; 2609:135-146. [PMID: 36515834 DOI: 10.1007/978-1-0716-2891-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Immunoprecipitation is an essential methodology for enriching and purifying targeted proteins and peptides for in-depth analysis by any number of further techniques, from Western blotting to mass spectrometry (MS). Historically, the posttranslational modification ADP-ribosylation (ADPr) has been studied mainly in its polymerized form (poly-ADPr), but recent studies support the abundance and physiological relevance of mono-ADPr. Here, we describe several approaches to enrich mono-ADP-ribosylated proteins and peptides using mono-ADPr-specific antibodies, which can be tailored to a desired target and mode of downstream analysis.
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62
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Zhang K, Peng T, Tao X, Tian M, Li Y, Wang Z, Ma S, Hu S, Pan X, Xue J, Luo J, Wu Q, Fu Y, Li S. Structural insights into caspase ADPR deacylization catalyzed by a bacterial effector and host calmodulin. Mol Cell 2022; 82:4712-4726.e7. [PMID: 36423631 DOI: 10.1016/j.molcel.2022.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/29/2022] [Accepted: 10/27/2022] [Indexed: 11/24/2022]
Abstract
Programmed cell death and caspase proteins play a pivotal role in host innate immune response combating pathogen infections. Blocking cell death is employed by many bacterial pathogens as a universal virulence strategy. CopC family type III effectors, including CopC from an environmental pathogen Chromobacterium violaceum, utilize calmodulin (CaM) as a co-factor to inactivate caspases by arginine ADPR deacylization. However, the molecular basis of the catalytic and substrate/co-factor binding mechanism is unknown. Here, we determine successive cryo-EM structures of CaM-CopC-caspase-3 ternary complex in pre-reaction, transition, and post-reaction states, which elucidate a multistep enzymatic mechanism of CopC-catalyzed ADPR deacylization. Moreover, we capture a snapshot of the detachment of modified caspase-3 from CopC. These structural insights are validated by mutagenesis analyses of CopC-mediated ADPR deacylization in vitro and animal infection in vivo. Our study offers a structural framework for understanding the molecular basis of arginine ADPR deacylization catalyzed by the CopC family.
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Affiliation(s)
- Kuo Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Ting Peng
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xinyuan Tao
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Miao Tian
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yanxin Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Zhao Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Shuaifei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Shufan Hu
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518055, Guangdong, China
| | - Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Jiwei Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qiulan Wu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China.
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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63
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Li R, Luo R, Luo Y, Hou Y, Wang J, Zhang Q, Chen X, Hu L, Zhou J. Biological function, mediate cell death pathway and their potential regulated mechanisms for post-mortem muscle tenderization of PARP1: A review. Front Nutr 2022; 9:1093939. [PMID: 36590225 PMCID: PMC9797534 DOI: 10.3389/fnut.2022.1093939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Tenderness is a key attribute of meat quality that affects consumers' willingness to purchase meat. Changes in the physiological environment of skeletal muscles following slaughter can disrupt the balance of redox homeostasis and may lead to cell death. Excessive accumulation of reactive oxygen species (ROS) in the myocytes causes DNA damage and activates poly ADP-ribose polymerase 1 (PARP1), which is involved in different intracellular metabolic pathways and is known to affect muscle tenderness during post-slaughter maturation. There is an urgent requirement to summarize the related research findings. Thus, this paper reviews the current research on the protein structure of PARP1 and its metabolism and activation, outlines the mechanisms underlying the function of PARP1 in regulating muscle tenderness through cysteine protease 3 (Caspase-3), oxidative stress, heat shock proteins (HSPs), and energy metabolism. In addition, we describe the mechanisms of PARP1 in apoptosis and necrosis pathways to provide a theoretical reference for enhancing the mature technology of post-mortem muscle tenderization.
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Affiliation(s)
- Rong Li
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Ruiming Luo
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Yulong Luo
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China,*Correspondence: Yulong Luo,
| | - Yanru Hou
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Jinxia Wang
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Qian Zhang
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Xueyan Chen
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Lijun Hu
- School of Food and Wine, Ningxia University, Yinchuan, China
| | - Julong Zhou
- School of Food and Wine, Ningxia University, Yinchuan, China
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64
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Jurėnas D, Rey M, Byrne D, Chamot-Rooke J, Terradot L, Cascales E. Salmonella antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of EF-Tu P-loop. Nucleic Acids Res 2022; 50:13114-13127. [PMID: 36484105 PMCID: PMC9825190 DOI: 10.1093/nar/gkac1162] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 11/11/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Rearrangement hot spot (Rhs) proteins are members of the broad family of polymorphic toxins. Polymorphic toxins are modular proteins composed of an N-terminal region that specifies their mode of secretion into the medium or into the target cell, a central delivery module, and a C-terminal domain that has toxic activity. Here, we structurally and functionally characterize the C-terminal toxic domain of the antibacterial Rhsmain protein, TreTu, which is delivered by the type VI secretion system of Salmonella enterica Typhimurium. We show that this domain adopts an ADP-ribosyltransferase fold and inhibits protein synthesis by transferring an ADP-ribose group from NAD+ to the elongation factor Tu (EF-Tu). This modification is specifically placed on the side chain of the conserved D21 residue located on the P-loop of the EF-Tu G-domain. Finally, we demonstrate that the TriTu immunity protein neutralizes TreTu activity by acting like a lid that closes the catalytic site and traps the NAD+.
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Affiliation(s)
- Dukas Jurėnas
- Correspondence may also be addressed to Dukas Jurėnas.
| | - Martial Rey
- Mass Spectrometry for Biology Unit, Université Paris Cité, Institut Pasteur, CNRS, UAR 2024, 75015 Paris, France
| | - Deborah Byrne
- Protein Expression Facility, Institut de Microbiologie de la Méditerranée (IMM), Aix-Marseille Université, CNRS, 13009 Marseille, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Université Paris Cité, Institut Pasteur, CNRS, UAR 2024, 75015 Paris, France
| | - Laurent Terradot
- Laboratory of Molecular Microbiology and Structural Biochemistry, Institut de Biologie et Chimie des Protéines, Centre National de la Recherche Scientifique, Université de Lyon, UMR 5086, 69367 Lyon, France
| | - Eric Cascales
- To whom correspondence should be addressed. Tel: +33 491164462; Fax: +33 491712124;
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Pillay N, Mariotti L, Zaleska M, Inian O, Jessop M, Hibbs S, Desfosses A, Hopkins PCR, Templeton CM, Beuron F, Morris EP, Guettler S. Structural basis of tankyrase activation by polymerization. Nature 2022; 612:162-169. [PMID: 36418402 PMCID: PMC9712121 DOI: 10.1038/s41586-022-05449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
Abstract
The poly-ADP-ribosyltransferase tankyrase (TNKS, TNKS2) controls a wide range of disease-relevant cellular processes, including WNT-β-catenin signalling, telomere length maintenance, Hippo signalling, DNA damage repair and glucose homeostasis1,2. This has incentivized the development of tankyrase inhibitors. Notwithstanding, our knowledge of the mechanisms that control tankyrase activity has remained limited. Both catalytic and non-catalytic functions of tankyrase depend on its filamentous polymerization3-5. Here we report the cryo-electron microscopy reconstruction of a filament formed by a minimal active unit of tankyrase, comprising the polymerizing sterile alpha motif (SAM) domain and its adjacent catalytic domain. The SAM domain forms a novel antiparallel double helix, positioning the protruding catalytic domains for recurring head-to-head and tail-to-tail interactions. The head interactions are highly conserved among tankyrases and induce an allosteric switch in the active site within the catalytic domain to promote catalysis. Although the tail interactions have a limited effect on catalysis, they are essential to tankyrase function in WNT-β-catenin signalling. This work reveals a novel SAM domain polymerization mode, illustrates how supramolecular assembly controls catalytic and non-catalytic functions, provides important structural insights into the regulation of a non-DNA-dependent poly-ADP-ribosyltransferase and will guide future efforts to modulate tankyrase and decipher its contribution to disease mechanisms.
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Affiliation(s)
- Nisha Pillay
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Mariola Zaleska
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Oviya Inian
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Matthew Jessop
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sam Hibbs
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Ambroise Desfosses
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Paul C R Hopkins
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK.
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK.
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66
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POLLARD CL, GIBB Z, SWEGEN A, GRUPEN CG. NAD +, Sirtuins and PARPs: enhancing oocyte developmental competence. J Reprod Dev 2022; 68:345-354. [PMID: 36171094 PMCID: PMC9792654 DOI: 10.1262/jrd.2022-052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Oocyte quality is the limiting factor in female fertility. It is well known that maternal nutrition plays a role in reproductive function, and manipulating nutrition to improve fertility in livestock has been common practice in the past, particularly with respect to negative energy balance in cattle. A deficiency in nicotinamide adenine dinucleotide (NAD+) production has been associated with increased incidences of miscarriage and congenital defects in humans and mice, while elevating NAD+ through dietary supplements in aged subjects improved oocyte quality and embryo development. NAD+ is consumed by Sirtuins and poly-ADP-ribose polymerases (PARPs) within the cell and thus need constant replenishment in order to maintain various cellular functions. Sirtuins and PARPs play important roles in oocyte maturation and embryo development, and their activation may prove beneficial to in vitro embryo production and livestock breeding programs. This review examines the roles of NAD+, Sirtuins and PARPs in aspects of fertility, providing insights into the potential use of NAD+-elevating treatments in livestock breeding and embryo production programs.
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Affiliation(s)
- Charley-Lea POLLARD
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, 2570, Australia
| | - Zamira GIBB
- Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Aleona SWEGEN
- Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Christopher G. GRUPEN
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, NSW, 2570, Australia
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Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J 2022; 289:7399-7410. [PMID: 34323016 PMCID: PMC9027952 DOI: 10.1111/febs.16142] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Daniela Corda
- Department of Biomedical Sciences, National Research Council, Rome, Italy
| | | | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Anthony R Fehr
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Nicolas C Hoch
- Department of Biochemistry, University of São Paulo, Brazil
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Ladurner
- Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Germany
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Norway
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joel Moss
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Friedrich Nolte
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Germany
| | - John Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, Canada
| | - Bryce M Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, NY, USA
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller University of Jena, Germany
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Roko Zaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
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68
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Activities and binding partners of E3 ubiquitin ligase DTX3L and its roles in cancer. Biochem Soc Trans 2022; 50:1683-1692. [DOI: 10.1042/bst20220501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Ubiquitination is a protein post-translational modification that affects protein localisation, stability and interactions. E3 ubiquitin ligases regulate the final step of the ubiquitination reaction by recognising target proteins and mediating the ubiquitin transfer from an E2 enzyme. DTX3L is a multi-domain E3 ubiquitin ligase in which the N-terminus mediates protein oligomerisation, a middle D3 domain mediates the interaction with PARP9, a RING domain responsible for recognising E2 ∼ Ub and a DTC domain has the dual activity of ADP-ribosylating ubiquitin and mediating ubiquitination. The activity of DTX3L is known to be modulated by at least two different factors: the concentration of NAD+, which dictates if the enzyme acts as a ligase or as an ADP-ribosyltransferase, and its binding partners, which affect DTX3L activity through yet unknown mechanisms. In light of recent findings it is possible that DTX3L could ubiquitinate ADP-ribose attached to proteins. Different DTX3L–protein complexes have been found to be part of multiple signalling pathways through which they promote the adhesion, proliferation, migration and chemoresistance of e.g. lymphoma, glioma, melanoma, and prostate cancer. In this review, we have covered the literature available for the molecular functions of DTX3L especially in the context of cancer biology, different pathways it regulates and how these relate to its function as an oncoprotein.
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69
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Role of PARP Inhibitors in Cancer Immunotherapy: Potential Friends to Immune Activating Molecules and Foes to Immune Checkpoints. Cancers (Basel) 2022; 14:cancers14225633. [PMID: 36428727 PMCID: PMC9688455 DOI: 10.3390/cancers14225633] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/19/2022] Open
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) induce cytotoxic effects as single agents in tumors characterized by defective repair of DNA double-strand breaks deriving from BRCA1/2 mutations or other abnormalities in genes associated with homologous recombination. Preclinical studies have shown that PARPi-induced DNA damage may affect the tumor immune microenvironment and immune-mediated anti-tumor response through several mechanisms. In particular, increased DNA damage has been shown to induce the activation of type I interferon pathway and up-regulation of PD-L1 expression in cancer cells, which can both enhance sensitivity to Immune Checkpoint Inhibitors (ICIs). Despite the recent approval of ICIs for a number of advanced cancer types based on their ability to reinvigorate T-cell-mediated antitumor immune responses, a consistent percentage of treated patients fail to respond, strongly encouraging the identification of combination therapies to overcome resistance. In the present review, we analyzed both established and unexplored mechanisms that may be elicited by PARPi, supporting immune reactivation and their potential synergism with currently used ICIs. This analysis may indicate novel and possibly patient-specific immune features that might represent new pharmacological targets of PARPi, potentially leading to the identification of predictive biomarkers of response to their combination with ICIs.
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70
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Alemasova EE, Lavrik OI. Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions. Int J Mol Sci 2022; 23:14075. [PMID: 36430551 PMCID: PMC9694962 DOI: 10.3390/ijms232214075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.
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Affiliation(s)
- Elizaveta E. Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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71
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Weixler L, Ikenga NJ, Voorneveld J, Aydin G, Bolte TMHR, Momoh J, Bütepage M, Golzmann A, Lüscher B, Filippov DV, Žaja R, Feijs KLH. Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used. Life Sci Alliance 2022; 6:6/1/e202201455. [PMID: 36368907 PMCID: PMC9652768 DOI: 10.26508/lsa.202201455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
The modification of substrates with ADP-ribose (ADPr) is important in, for example, antiviral immunity and cancer. Recently, several reagents were developed to detect ADP-ribosylation; however, it is unknown whether they recognise ADPr, specific amino acid-ADPr linkages, or ADPr with the surrounding protein backbone. We first optimised methods to prepare extracts containing ADPr-proteins and observe that depending on the amino acid modified, the modification is heatlabile. We tested the reactivity of available reagents with diverse ADP-ribosylated protein and RNA substrates and observed that not all reagents are equally suited for all substrates. Next, we determined cross-reactivity with adenylylated RNA, AMPylated proteins, and metabolites, including NADH, which are detected by some reagents. Lastly, we analysed ADP-ribosylation using confocal microscopy, where depending on the fixation method, either mitochondrion, nucleus, or nucleolus is stained. This study allows future work dissecting the function of ADP-ribosylation in cells, both on protein and on RNA substrates, as we optimised sample preparation methods and have defined the reagents suitable for specific methods and substrates.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Nonso Josephat Ikenga
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Gülcan Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Timo MHR Bolte
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Alexandra Golzmann
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Karla LH Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany,Correspondence: ;
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72
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Alemasova EE, Lavrik OI. A sePARate phase? Poly(ADP-ribose) versus RNA in the organization of biomolecular condensates. Nucleic Acids Res 2022; 50:10817-10838. [PMID: 36243979 PMCID: PMC9638928 DOI: 10.1093/nar/gkac866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 10/09/2022] [Indexed: 11/13/2022] Open
Abstract
Condensates are biomolecular assemblies that concentrate biomolecules without the help of membranes. They are morphologically highly versatile and may emerge via distinct mechanisms. Nucleic acids-DNA, RNA and poly(ADP-ribose) (PAR) play special roles in the process of condensate organization. These polymeric scaffolds provide multiple specific and nonspecific interactions during nucleation and 'development' of macromolecular assemblages. In this review, we focus on condensates formed with PAR. We discuss to what extent the literature supports the phase separation origin of these structures. Special attention is paid to similarities and differences between PAR and RNA in the process of dynamic restructuring of condensates during their functioning.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
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73
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Di Paola S, Matarese M, Barretta ML, Dathan N, Colanzi A, Corda D, Grimaldi G. PARP10 Mediates Mono-ADP-Ribosylation of Aurora-A Regulating G2/M Transition of the Cell Cycle. Cancers (Basel) 2022; 14:5210. [PMID: 36358629 PMCID: PMC9659153 DOI: 10.3390/cancers14215210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/11/2022] [Accepted: 10/22/2022] [Indexed: 08/13/2023] Open
Abstract
Intracellular mono-ADP-ribosyltransferases (mono-ARTs) catalyze the covalent attachment of a single ADP-ribose molecule to protein substrates, thus regulating their functions. PARP10 is a soluble mono-ART involved in the modulation of intracellular signaling, metabolism and apoptosis. PARP10 also participates in the regulation of the G1- and S-phase of the cell cycle. However, the role of this enzyme in G2/M progression is not defined. In this study, we found that genetic ablation, protein depletion and pharmacological inhibition of PARP10 cause a delay in the G2/M transition of the cell cycle. Moreover, we found that the mitotic kinase Aurora-A, a previously identified PARP10 substrate, is actively mono-ADP-ribosylated (MARylated) during G2/M transition in a PARP10-dependent manner. Notably, we showed that PARP10-mediated MARylation of Aurora-A enhances the activity of the kinase in vitro. Consistent with an impairment in the endogenous activity of Aurora-A, cells lacking PARP10 show a decreased localization of the kinase on the centrosomes and mitotic spindle during G2/M progression. Taken together, our data provide the first evidence of a direct role played by PARP10 in the progression of G2 and mitosis, an event that is strictly correlated to the endogenous MARylation of Aurora-A, thus proposing a novel mechanism for the modulation of Aurora-A kinase activity.
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Affiliation(s)
- Simone Di Paola
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Maria Matarese
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Maria Luisa Barretta
- National Research Council (CNR), Piazzale Aldo Moro, 700185 Rome, Italy
- Steril Farma Srl, Via L. Da Vinci 128, 80055 Portici, Italy
| | - Nina Dathan
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Antonino Colanzi
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Daniela Corda
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
| | - Giovanna Grimaldi
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy
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74
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Zhu K, Suskiewicz MJ, Hloušek-Kasun A, Meudal H, Mikoč A, Aucagne V, Ahel D, Ahel I. DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on protein substrates. SCIENCE ADVANCES 2022; 8:eadd4253. [PMID: 36197986 PMCID: PMC7615817 DOI: 10.1126/sciadv.add4253] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitylation had been considered limited to protein lysine residues, but other substrates have recently emerged. Here, we show that DELTEX E3 ligases specifically target the 3' hydroxyl of the adenosine diphosphate (ADP)-ribosyl moiety that can be linked to a protein, thus generating a hybrid ADP-ribosyl-ubiquitin modification. Unlike other known hydroxyl-specific E3s, which proceed via a covalent E3~ubiqutin intermediate, DELTEX enzymes are RING E3s that stimulate a direct ubiquitin transfer from E2~ubiquitin onto a substrate. However, DELTEXes follow a previously unidentified paradigm for RING E3s, whereby the ligase not only forms a scaffold but also provides catalytic residues to activate the acceptor. Comparative analysis of known hydroxyl-ubiquitylating active sites points to the recurring use of a catalytic histidine residue, which, in DELTEX E3s, is potentiated by a glutamate in a catalytic triad-like manner. In addition, we determined the hydrolase specificity profile of this modification, identifying human and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enzymes that could reverse it in cells.
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Affiliation(s)
- Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Marcin J. Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | | | - Hervé Meudal
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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75
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Kurgina TA, Moor NA, Kutuzov MM, Lavrik OI. The HPF1-dependent histone PARylation catalyzed by PARP2 is specifically stimulated by an incised AP site-containing BER DNA intermediate. DNA Repair (Amst) 2022; 120:103423. [DOI: 10.1016/j.dnarep.2022.103423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/03/2022]
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76
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PARP-1 Is a Potential Marker of Retinal Photooxidation and a Key Signal Regulator in Retinal Light Injury. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6881322. [PMID: 36124087 PMCID: PMC9482536 DOI: 10.1155/2022/6881322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 12/02/2022]
Abstract
Advancements in technology have resulted in increasing concerns over the safety of eye exposure to light illumination, since prolonged exposure to intensive visible light, especially to short-wavelength light in the visible spectrum, can cause photochemical damage to the retina through a photooxidation-triggered cascade reaction. Poly(ADP-ribose) polymerase-1 (PARP-1) is the ribozyme responsible for repairing DNA damage. When damage to DNA occurs, including nicks and breaks, PARP-1 is rapidly activated, synthesizing a large amount of PAR and recruiting other nuclear factors to repair the damaged DNA. However, retinal photochemical damage may lead to the overactivation of PARP-1, triggering PARP-dependent cell death, including parthanatos, necroptosis, and autophagy. In this review, we retrieved targeted articles with the keywords such as “PARP-1,” “photoreceptor,” “retinal light damage,” and “photooxidation” from databases and summarized the molecular mechanisms involved in retinal photooxidation, PARP activation, and DNA repair to clarify the key regulatory role of PARP-1 in retinal light injury and to determine whether PARP-1 may be a potential marker in response to retinal photooxidation. The highly sensitive detection of PARP-1 activity may facilitate early evaluation of the effects of light on the retina, which will provide an evidentiary basis for the future assessment of the safety of light illumination from optoelectronic products and medical devices.
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77
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Zong W, Gong Y, Sun W, Li T, Wang ZQ. PARP1: Liaison of Chromatin Remodeling and Transcription. Cancers (Basel) 2022; 14:cancers14174162. [PMID: 36077699 PMCID: PMC9454564 DOI: 10.3390/cancers14174162] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a covalent post-translational modification and plays a key role in the immediate response of cells to stress signals. Poly(ADP-ribose) polymerase 1 (PARP1), the founding member of the PARP superfamily, synthesizes long and branched polymers of ADP-ribose (PAR) onto acceptor proteins, thereby modulating their function and their local surrounding. PARP1 is the most prominent of the PARPs and is responsible for the production of about 90% of PAR in the cell. Therefore, PARP1 and PARylation play a pleotropic role in a wide range of cellular processes, such as DNA repair and genomic stability, cell death, chromatin remodeling, inflammatory response and gene transcription. PARP1 has DNA-binding and catalytic activities that are important for DNA repair, yet also modulate chromatin conformation and gene transcription, which can be independent of DNA damage response. PARP1 and PARylation homeostasis have also been implicated in multiple diseases, including inflammation, stroke, diabetes and cancer. Studies of the molecular action and biological function of PARP1 and PARylation provide a basis for the development of pharmaceutic strategies for clinical applications. This review focuses primarily on the role of PARP1 in the regulation of chromatin remodeling and transcriptional activation.
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Affiliation(s)
- Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Correspondence: (W.Z.); or (Z.-Q.W.)
| | - Yamin Gong
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- College of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, 07743 Jena, Germany
- Correspondence: (W.Z.); or (Z.-Q.W.)
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78
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Weixler L, Feijs KLH, Zaja R. ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs. Nucleic Acids Res 2022; 50:9426-9441. [PMID: 36018800 PMCID: PMC9458441 DOI: 10.1093/nar/gkac711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 12/24/2022] Open
Abstract
RNA function relies heavily on posttranscriptional modifications. Recently, it was shown that certain PARPs and TRPT1 can ADP-ribosylate RNA in vitro. Traditionally, intracellular ADP-ribosylation has been considered mainly as a protein posttranslational modification. To date, it is not clear whether RNA ADP-ribosylation occurs in cells. Here we present evidence that different RNA species are ADP-ribosylated in human cells. The modification of cellular RNA is mediated by several transferases such as TRPT1, PARP10, PARP11, PARP12 and PARP15 and is counteracted by different hydrolases including TARG1, PARG and ARH3. In addition, diverse cellular stressors can modulate the content of ADP-ribosylated RNA in cells. We next investigated potential consequences of ADP-ribosylation for RNA and found that ADPr-capped mRNA is protected against XRN1 mediated degradation but is not translated. T4 RNA ligase 1 can ligate ADPr-RNA in absence of ATP, resulting in the incorporation of an abasic site. We thus provide the first evidence of RNA ADP-ribosylation in mammalian cells and postulate potential functions of this novel RNA modification.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen 52074, Germany
| | - Karla L H Feijs
- Correspondence may also be addressed to Karla L.H. Feijs. Tel: +49 2418080692; Fax: +49 2418082427;
| | - Roko Zaja
- To whom correspondence should be addressed. Tel: +49 2418037944; Fax: +49 2418082427;
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79
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Rouleau-Turcotte É, Krastev DB, Pettitt SJ, Lord CJ, Pascal JM. Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery. Mol Cell 2022; 82:2939-2951.e5. [PMID: 35793673 PMCID: PMC9391306 DOI: 10.1016/j.molcel.2022.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/29/2022] [Accepted: 06/08/2022] [Indexed: 01/02/2023]
Abstract
PARP1 rapidly detects DNA strand break damage and allosterically signals break detection to the PARP1 catalytic domain to activate poly(ADP-ribose) production from NAD+. PARP1 activation is characterized by dynamic changes in the structure of a regulatory helical domain (HD); yet, there are limited insights into the specific contributions that the HD makes to PARP1 allostery. Here, we have determined crystal structures of PARP1 in isolated active states that display specific HD conformations. These captured snapshots and biochemical analysis illustrate HD contributions to PARP1 multi-domain and high-affinity interaction with DNA damage, provide novel insights into the mechanics of PARP1 allostery, and indicate how HD active conformations correspond to alterations in the catalytic region that reveal the active site to NAD+. Our work deepens the understanding of PARP1 catalytic activation, the dynamics of the binding site of PARP inhibitor compounds, and the mechanisms regulating PARP1 retention on DNA damage.
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Affiliation(s)
- Élise Rouleau-Turcotte
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Dragomir B Krastev
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London SW3 6JB, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London SW3 6JB, UK
| | - Christopher J Lord
- CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London SW3 6JB, UK
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada.
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80
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Bernardini I, Fabrello J, Vecchiato M, Ferraresso S, Babbucci M, Peruzza L, Rovere GD, Masiero L, Marin MG, Bargelloni L, Gambaro A, Patarnello T, Matozzo V, Milan M. Effects of environmental concentrations of the fragrance amyl salicylate on the mediterranean mussel Mytilus galloprovincialis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119502. [PMID: 35605833 DOI: 10.1016/j.envpol.2022.119502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Amyl salicylate (AS) is a fragrance massively used as a personal care product and following the discharged in wastewaters may end up in the aquatic environment representing a potential threat for the ecosystem and living organisms. AS was recently detected in water of the Venice Lagoon, a vulnerable area continuously subjected to the income of anthropogenic chemicals. The lagoon is a relevant area for mollusc farming, including the Mediterranean mussels (Mytilus galloprovincialis) having an important economic and ecological role. Despite high levels of AS occurred in water of the Lagoon of Venice, no studies investigated the possible consequences of AS exposures on species inhabiting this ecosystem to date. For the first time, we applied a multidisciplinary approach to investigate the potential effects of the fragrance AS on Mediterranean mussels. To reach such a goal, bioaccumulation, cellular, biochemical, and molecular analyses (RNA-seq and microbiota characterization) were measured in mussels treated for 7 and 14 days with different AS Venice lagoon environmental levels (0.1 and 0.5 μg L-1). Despite chemical investigations suggested low AS bioaccumulation capability, cellular and molecular analyses highlighted the disruption of several key cellular processes after the prolonged exposures to the high AS concentration. Among them, potential immunotoxicity and changes in transcriptional regulation of pathways involved in energy metabolism, stress response, apoptosis and cell death regulations have been observed. Conversely, exposure to the low AS concentration demonstrated weak transcriptional changes and transient increased representation of opportunistic pathogens, as Arcobacter genus and Vibrio aestuarianus. Summarizing, this study provides the first overview on the effects of AS on one of the most widely farmed mollusk species.
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Affiliation(s)
- I Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - J Fabrello
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy
| | - M Vecchiato
- Institute of Polar Sciences - National Research Council (ISP-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy; Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - M Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - L Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - L Masiero
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy
| | - M G Marin
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - A Gambaro
- Institute of Polar Sciences - National Research Council (ISP-CNR), Via Torino 155, 30172, Venezia-Mestre, Venice, Italy; Department of Environmental Sciences, Informatics and Statistics (DAIS), Ca' Foscari University of Venice, Via Torino 155, 30172, Venezia-Mestre, Venice, Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
| | - V Matozzo
- Department of Biology, University of Padova, Via Bassi 58/B, 35131, Padova, Italy.
| | - M Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, PD, Italy
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81
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Revisiting PARP2 and PARP1 trapping through quantitative live-cell imaging. Biochem Soc Trans 2022; 50:1169-1177. [PMID: 35959996 DOI: 10.1042/bst20220366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) and 2 (PARP2) are two DNA damage-induced poly (ADP-ribose) (PAR) polymerases in cells and are the targets of PARP inhibitors used for cancer therapy. Strand breaks recruit and activate PARP1 and 2, which rapidly generate PAR from NAD+. PAR promotes the recruitment of other repair factors, relaxes chromatin, and has a role in DNA repair, transcription regulation, and RNA biology. Four PARP1/2 dual inhibitors are currently used to treat BRCA-deficient breast, ovarian, prostate, and pancreatic cancers. In addition to blocking the enzymatic activity of PARP1 and 2, clinical PARP inhibitors extend the appearance of PARP1 and PARP2 on chromatin after damage, termed trapping. Loss of PARP1 confers resistance to PARP inhibitors, suggesting an essential role of trapping in cancer therapy. Yet, whether the persistent PARP1 and 2 foci at the DNA damage sites are caused by the retention of the same molecules or by the continual exchange of different molecules remains unknown. Here, we discuss recent results from quantitative live-cell imaging studies focusing on PARP1 and PARP2's distinct DNA substrate specificities and modes of recruitment and trapping with implications for cancer therapy and on-target toxicities of PARP inhibitors.
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82
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Li P, Lei Y, Qi J, Liu W, Yao K. Functional roles of ADP-ribosylation writers, readers and erasers. Front Cell Dev Biol 2022; 10:941356. [PMID: 36035988 PMCID: PMC9404506 DOI: 10.3389/fcell.2022.941356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
ADP-ribosylation is a reversible post-translational modification (PTM) tightly regulated by the dynamic interplay between its writers, readers and erasers. As an intricate and versatile PTM, ADP-ribosylation plays critical roles in various physiological and pathological processes. In this review, we discuss the major players involved in the ADP-ribosylation cycle, which may facilitate the investigation of the ADP-ribosylation function and contribute to the understanding and treatment of ADP-ribosylation associated disease.
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83
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Zhang Y, Fang M, Li S, Xu H, Ren J, Tu L, Zuo B, Yao W, Liang G. BTApep-TAT peptide inhibits ADP-ribosylation of BORIS to induce DNA damage in cancer. Mol Cancer 2022; 21:158. [PMID: 35918747 PMCID: PMC9344678 DOI: 10.1186/s12943-022-01621-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brother of regulator of imprinted sites (BORIS) is expressed in most cancers and often associated with short survival and poor prognosis in patients. BORIS inhibits apoptosis and promotes proliferation of cancer cells. However, its mechanism of action has not been elucidated, and there is no known inhibitor of BORIS. METHODS A phage display library was used to find the BORIS inhibitory peptides and BTApep-TAT was identified. The RNA sequencing profile of BTApep-TAT-treated H1299 cells was compared with that of BORIS-knockdown cells. Antitumor activity of BTApep-TAT was evaluated in a non-small cell lung cancer (NSCLC) xenograft mouse model. BTApep-TAT was also used to investigate the post-translational modification (PTM) of BORIS and the role of BORIS in DNA damage repair. Site-directed mutants of BORIS were constructed and used for investigating PTM and the function of BORIS. RESULTS BTApep-TAT induced DNA damage in cancer cells and suppressed NSCLC xenograft tumor progression. Investigation of the mechanism of action of BTApep-TAT demonstrated that BORIS underwent ADP ribosylation upon double- or single-strand DNA damage. Substitution of five conserved glutamic acid (E) residues with alanine residues (A) between amino acids (AAs) 198 and 228 of BORIS reduced its ADP ribosylation. Inhibition of ADP ribosylation of BORIS by a site-specific mutation or by BTApep-TAT treatment blocked its interaction with Ku70 and impaired the function of BORIS in DNA damage repair. CONCLUSIONS The present study identified an inhibitor of BORIS, highlighted the importance of ADP ribosylation of BORIS, and revealed a novel function of BORIS in DNA damage repair. The present work provides a practical method for the future screening or optimization of drugs targeting BORIS.
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Affiliation(s)
- Yanmei Zhang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.
| | - Mengdie Fang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.,College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Shouye Li
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China.,Zhejiang Eyoung Pharmaceutical Research and Development Center, Hangzhou, 311258, Zhejiang, China
| | - Hao Xu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Juan Ren
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Linglan Tu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Bowen Zuo
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Wanxin Yao
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China
| | - Guang Liang
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, 310013, China. .,College of Pharmacy, Hangzhou Medical College, Hangzhou, 311300, Zhejiang, China.
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84
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Zhou X, Yang Y, Xu Q, Zhou H, Zhong F, Deng J, Zhang J, Li J. Crystal structures of the catalytic domain of human PARP15 in complex with small molecule inhibitors. Biochem Biophys Res Commun 2022; 622:93-100. [PMID: 35843099 DOI: 10.1016/j.bbrc.2022.06.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/25/2022]
Abstract
PARP15, or ARTD7, is an enzyme carrying out mono-ADP-ribosylation and regulating activities of a range of cellular proteins. This enzyme belongs to the family of the poly(ADP-ribose) polymerases (PARPs), which comprises of proteins with various potential disease indications. Due to their involvement in a number of cellular processes and important role in DNA repair and regulation, PARPs have been considered attractive therapeutic targets over the past few years. The pursuit of small molecule PARP inhibitors has resulted in several FDA approved drugs for multiple cancers so far. As the use of PARP inhibitors as drug scaffolds is actively explored recently, there is increasing interest in the design of selective inhibitors based on the structural features of the PARP proteins. Here, we solved high-resolution crystal structures of the human PARP15 catalytic domain in complex with three marketed drugs of PARP inhibitors, which includes compounds 3-AB, iniparib and niraparib. The structures reported here contribute to our understanding of the ligand binding modes and structural features in the PARP15 catalytic domain, which can be employed to guide the rational design of selective inhibitors of PARPs.
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Affiliation(s)
- Xuelan Zhou
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Yang Yang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China
| | - Qin Xu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Fanglin Zhong
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou, 341000, China
| | - Jun Deng
- The First Affiliated Hospital of Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Jin Zhang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou, 341000, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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85
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Recent advances in structural types and medicinal chemistry of PARP-1 inhibitors. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02919-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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86
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Nizi M, Maksimainen MM, Lehtiö L, Tabarrini O. Medicinal Chemistry Perspective on Targeting Mono-ADP-Ribosylating PARPs with Small Molecules. J Med Chem 2022; 65:7532-7560. [PMID: 35608571 PMCID: PMC9189837 DOI: 10.1021/acs.jmedchem.2c00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Indexed: 12/13/2022]
Abstract
Major advances have recently defined functions for human mono-ADP-ribosylating PARP enzymes (mono-ARTs), also opening up potential applications for targeting them to treat diseases. Structural biology combined with medicinal chemistry has allowed the design of potent small molecule inhibitors which typically bind to the catalytic domain. Most of these inhibitors are at the early stages, but some have already a suitable profile to be used as chemical tools. One compound targeting PARP7 has even progressed to clinical trials. In this review, we collect inhibitors of mono-ARTs with a typical "H-Y-Φ" motif (Φ = hydrophobic residue) and focus on compounds that have been reported as active against one or a restricted number of enzymes. We discuss them from a medicinal chemistry point of view and include an analysis of the available crystal structures, allowing us to craft a pharmacophore model that lays the foundation for obtaining new potent and more specific inhibitors.
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Affiliation(s)
- Maria
Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, 06123 Perugia, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 5400 Oulu, Finland
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 5400 Oulu, Finland
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, 06123 Perugia, Italy
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87
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Minnee H, Rack JGM, van der Marel GA, Overkleeft HS, Codée JDC, Ahel I, Filippov DV. Mimetics of ADP-Ribosylated Histidine through Copper(I)-Catalyzed Click Chemistry. Org Lett 2022; 24:3776-3780. [PMID: 35587229 PMCID: PMC9171823 DOI: 10.1021/acs.orglett.2c01300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/28/2022]
Abstract
A convergent synthesis provided nearly perfect τ-ADP-ribosylated histidine isosteres (His*-τ-ADPr) via a copper(I)-catalyzed cycloaddition between an azido-ADP-ribosyl analogue and an oligopeptide carrying a propargyl glycine. Both α- and β-configured azido-ADP-ribosyl analogues have been synthesized. The former required participation of the C-2 ester functionality during glycosylation, while the latter was obtained in high stereoselectivity from an imidate donor with a nonparticipating para-methoxy benzyl ether. Four His*-τ-ADPr peptides were screened against a library of human ADP-ribosyl hydrolases.
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Affiliation(s)
- Hugo Minnee
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes G. M. Rack
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Gijsbert A. van der Marel
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Herman S. Overkleeft
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jeroen D. C. Codée
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Dmitri V. Filippov
- Bio-Organic
Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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88
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Luo L, Keyomarsi K. PARP inhibitors as single agents and in combination therapy: the most promising treatment strategies in clinical trials for BRCA-mutant ovarian and triple-negative breast cancers. Expert Opin Investig Drugs 2022; 31:607-631. [PMID: 35435784 PMCID: PMC9296104 DOI: 10.1080/13543784.2022.2067527] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Poly (ADP-ribose) polymerase inhibitors (PARPis) are an exciting class of agents that have shown efficacy, particularly for BRCA-mutant triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSOC). However, most patients who receive PARPi as their standard of care therapy inevitably develop resistance and this underscores the need to identify additional targets that can circumvent such resistance. Combination treatment strategies have been developed in preclinical and clinical studies to address the challenges of efficacy and resistance. AREAS COVERED This review examines completed or ongoing clinical trials of PARPi mono- and combination therapies. PARPi monotherapy in HER2 negative breast (HR+ and TNBC subtypes) and ovarian cancer is a focal point. The authors propose potential strategies that might overcome resistance to PARPi and discuss key questions and future directions. EXPERT OPINION While the advent of PARPis has significantly improved the treatment of tumors with defects in DNA damage and repair pathways, careful patient selection will be essential to enhance these treatments. The identification of molecular biomarkers to predict disease response and progression is an endeavor.
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Affiliation(s)
- Linjie Luo
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khandan Keyomarsi
- Department of Experimental Radiation Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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89
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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90
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Lehner M, Rieth S, Höllmüller E, Spliesgar D, Mertes B, Stengel F, Marx A. Profiling of the ADP-Ribosylome in Living Cells. Angew Chem Int Ed Engl 2022; 61:e202200977. [PMID: 35188710 PMCID: PMC9315028 DOI: 10.1002/anie.202200977] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Indexed: 12/12/2022]
Abstract
Post-translational modification (PTM) with ADP-ribose and poly(ADP-ribose) using nicotinamide adenine dinucleotide (NAD+ ) as substrate is involved in the regulation of numerous cellular pathways in eukaryotes, notably the response to DNA damage caused by cellular stress. Nevertheless, due to intrinsic properties of NAD+ e.g., high polarity and associated poor cell passage, these PTMs are difficult to characterize in cells. Here, two new NAD+ derivatives are presented, which carry either a fluorophore or an affinity tag and, in combination with developed methods for mild cell delivery, allow studies in living human cells. We show that this approach allows not only the imaging of ADP-ribosylation in living cells but also the proteome-wide analysis of cellular adaptation by protein ADP-ribosylation as a consequence of environmental changes such as H2 O2 -induced oxidative stress or the effect of the approved anti-cancer drug olaparib. Our results therefore pave the way for further functional and clinical studies of the ADP-ribosylated proteome in living cells in health and disease.
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Affiliation(s)
- Maike Lehner
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
| | - Sonja Rieth
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
| | - Eva Höllmüller
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
| | - Daniel Spliesgar
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
| | - Bastian Mertes
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
| | - Florian Stengel
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
| | - Andreas Marx
- Departments of Chemistry and BiologyKonstanz Research School Chemical BiologyUniversitätsstraße 1078457KonstanzGermany
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91
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Lin X, Jiang W, Rudolph J, Lee BJ, Luger K, Zha S. PARP inhibitors trap PARP2 and alter the mode of recruitment of PARP2 at DNA damage sites. Nucleic Acids Res 2022; 50:3958-3973. [PMID: 35349716 PMCID: PMC9023293 DOI: 10.1093/nar/gkac188] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Dual-inhibitors of PARP1 and PARP2 are promising anti-cancer drugs. In addition to blocking PARP1&2 enzymatic activity, PARP inhibitors also extend the lifetime of DNA damage-induced PARP1&2 foci, termed trapping. Trapping is important for the therapeutic effects of PARP inhibitors. Using live-cell imaging, we found that PARP inhibitors cause persistent PARP2 foci by switching the mode of PARP2 recruitment from a predominantly PARP1- and PAR-dependent rapid exchange to a WGR domain-mediated stalling of PARP2 on DNA. Specifically, PARP1-deletion markedly reduces but does not abolish PARP2 foci. The residual PARP2 foci in PARP1-deficient cells are DNA-dependent and abrogated by the R140A mutation in the WGR domain. Yet, PARP2-R140A forms normal foci in PARP1-proficient cells. In PARP1-deficient cells, PARP inhibitors - niraparib, talazoparib, and, to a lesser extent, olaparib - enhance PARP2 foci by preventing PARP2 exchange. This trapping of PARP2 is independent of auto-PARylation and is abolished by the R140A mutation in the WGR domain and the H415A mutation in the catalytic domain. Taken together, we found that PARP inhibitors trap PARP2 by physically stalling PARP2 on DNA via the WGR-DNA interaction while suppressing the PARP1- and PAR-dependent rapid exchange of PARP2.
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Affiliation(s)
- Xiaohui Lin
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Wenxia Jiang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
| | - Brian J Lee
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO80309, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO80309, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
- Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY10032, USA
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92
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Abstract
Post-translational modifications exist in different varieties to regulate diverse characteristics of their substrates, ultimately leading to maintenance of cell health. The enzymes of the intracellular poly(ADP-ribose) polymerase (PARP) family can transfer either a single ADP-ribose to targets, in a reaction called mono(ADP-ribosyl)ation or MARylation, or multiple to form chains of poly(ADP-ribose) or PAR. Traditionally thought to be attached to arginine or glutamate, recent data have added serine, tyrosine, histidine and others to the list of potential ADP-ribose acceptor amino acids. PARylation by PARP1 has been relatively well studied, whereas less is known about the other family members such as PARP7 and PARP10. ADP-ribosylation on arginine and serine is reversed by ARH1 and ARH3 respectively, whereas macrodomain-containing MACROD1, MACROD2 and TARG1 reverse modification of acidic residues. For the other amino acids, no hydrolases have been identified to date. For many PARPs, it is not clear yet what their endogenous targets are. Better understanding of their biochemical reactions is required to be able to determine their biological functions in future studies. In this review, we discuss the current knowledge of PARP specificity in vitro and in cells, as well as provide an outlook for future research.
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93
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Muoio D, Laspata N, Fouquerel E. Functions of ADP-ribose transferases in the maintenance of telomere integrity. Cell Mol Life Sci 2022; 79:215. [PMID: 35348914 PMCID: PMC8964661 DOI: 10.1007/s00018-022-04235-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/21/2022]
Abstract
The ADP-ribose transferase (ART) family comprises 17 enzymes that catalyze mono- or poly-ADP-ribosylation, a post-translational modification of proteins. Present in all subcellular compartments, ARTs are implicated in a growing number of biological processes including DNA repair, replication, transcription regulation, intra- and extra-cellular signaling, viral infection and cell death. Five members of the family, PARP1, PARP2, PARP3, tankyrase 1 and tankyrase 2 are mainly described for their crucial functions in the maintenance of genome stability. It is well established that the most describedrole of PARP1, 2 and 3 is the repair of DNA lesions while tankyrases 1 and 2 are crucial for maintaining the integrity of telomeres. Telomeres, nucleoprotein complexes located at the ends of eukaryotic chromosomes, utilize their unique structure and associated set of proteins to orchestrate the mechanisms necessary for their own protection and replication. While the functions of tankyrases 1 and 2 at telomeres are well known, several studies have also brought PARP1, 2 and 3 to the forefront of telomere protection. The singular quality of the telomeric environment has highlighted protein interactions and molecular pathways distinct from those described throughout the genome. The aim of this review is to provide an overview of the current knowledge on the multiple roles of PARP1, PARP2, PARP3, tankyrase 1 and tankyrase 2 in the maintenance and preservation of telomere integrity.
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Affiliation(s)
- Daniela Muoio
- UPMC Cancer Institute and Department of Pharmacology and Chemical Biology at the University of Pittsburgh, Hillman Cancer Center, 5115 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Natalie Laspata
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 S. 10th street, Philadelphia, PA, 19107, USA
| | - Elise Fouquerel
- UPMC Cancer Institute and Department of Pharmacology and Chemical Biology at the University of Pittsburgh, Hillman Cancer Center, 5115 Centre Avenue, Pittsburgh, PA, 15213, USA.
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94
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Yu M, Yang Y, Sykes M, Wang S. Small-Molecule Inhibitors of Tankyrases as Prospective Therapeutics for Cancer. J Med Chem 2022; 65:5244-5273. [PMID: 35306814 DOI: 10.1021/acs.jmedchem.1c02139] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tankyrases are multifunctional poly(adenosine diphosphate-ribose) polymerases that regulate diverse biological processes including telomere maintenance and cellular signaling. These processes are often implicated in a number of human diseases, with cancer being the most prevalent example. Accordingly, tankyrase inhibitors have gained increasing attention as potential therapeutics. Since the discovery of XAV939 and IWR-1 as the first tankyrase inhibitors over two decades ago, tankyrase-targeted drug discovery has made significant progress. This review starts with an introduction of tankyrases, with emphasis placed on their cancer-related functions. Small-molecule inhibitors of tankyrases are subsequently delineated based on their distinct modes of binding to the enzymes. In addition to inhibitors that compete with oxidized nicotinamide adenine dinucleotide (NAD+) for binding to the catalytic domain of tankyrases, non-NAD+-competitive inhibitors are detailed. This is followed by a description of three clinically trialled tankyrase inhibitors. To conclude, some of challenges and prospects in developing tankyrase-targeted cancer therapies are discussed.
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Affiliation(s)
- Mingfeng Yu
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Yuchao Yang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew Sykes
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
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95
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Abstract
PARP is an important target in the treatment of cancers, particularly in patients with breast, ovarian, or prostate cancer that have compromised homologous recombination repair (i.e., BRCA−/−). This review about inhibitors of PARP (PARPi) is for readers interested in the development of next-generation drugs for the treatment of cancer, providing insights into structure–activity relationships, in vitro vs. in vivo potency, PARP trapping, and synthetic lethality. Selective inhibitors of PARP1 and PARP2 (PARP1/2) are used to treat cancer patients with deficiencies in the repair of DNA via homologous recombination. Here we provide a perspective on the reported potencies of the most studied of these inhibitors (olaparib, talazoparib, niraparib, rucaparib, and veliparib) in vitro and in vivo and how these numbers relate to the known structures of these inhibitors bound to the active sites of PARP1 and PARP2. We suggest that the phenomenon of PARP trapping is primarily due to the inhibition of the catalytic activity of PARP1 and that the basis for the higher potency of talazoparib compared to the other inhibitors lies in its more extensive network of interactions with conserved residues in the active site. We also consider the potential role of the recently characterized protein “Histone PARylation Factor 1” (HPF1), which interacts with PARP1/2 to form a shared active site, for the design of the next generation of inhibitors of PARP1/2.
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96
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Manco G, Lacerra G, Porzio E, Catara G. ADP-Ribosylation Post-Translational Modification: An Overview with a Focus on RNA Biology and New Pharmacological Perspectives. Biomolecules 2022; 12:biom12030443. [PMID: 35327636 PMCID: PMC8946771 DOI: 10.3390/biom12030443] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cellular functions are regulated through the gene expression program by the transcription of new messenger RNAs (mRNAs), alternative RNA splicing, and protein synthesis. To this end, the post-translational modifications (PTMs) of proteins add another layer of complexity, creating a continuously fine-tuned regulatory network. ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules, regulating a multitude of key functional processes as diverse as DNA damage repair (DDR), transcriptional regulation, intracellular transport, immune and stress responses, and cell survival. Additionally, due to the emerging role of ADP-ribosylation in pathological processes, ADP-ribosyltransferases (ARTs), the enzymes involved in ADPr, are attracting growing interest as new drug targets. In this review, an overview of human ARTs and their related biological functions is provided, mainly focusing on the regulation of ADP-ribosyltransferase Diphtheria toxin-like enzymes (ARTD)-dependent RNA functions. Finally, in order to unravel novel gene functional relationships, we propose the analysis of an inventory of human gene clusters, including ARTDs, which share conserved sequences at 3′ untranslated regions (UTRs).
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Affiliation(s)
- Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
- Correspondence: (G.M.); (G.C.)
| | - Giuseppina Lacerra
- Institute of Genetics and Biophysics “Adriano Buzzati-Traverso”, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
| | - Elena Porzio
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy;
- Correspondence: (G.M.); (G.C.)
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97
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Lehner M, Rieth S, Höllmüller E, Spliesgar D, Mertes B, Stengel F, Marx A. Profiling of the ADP‐Ribosylome in Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Maike Lehner
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
| | - Sonja Rieth
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
| | - Eva Höllmüller
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
| | - Daniel Spliesgar
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
| | - Bastian Mertes
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
| | - Florian Stengel
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
| | - Andreas Marx
- Departments of Chemistry and Biology Konstanz Research School Chemical Biology Universitätsstraße 10 78457 Konstanz Germany
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98
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Cardamone MD, Gao Y, Kwan J, Hayashi V, Sheeran M, Xu J, English J, Orofino J, Emili A, Perissi V. Neuralized-like protein 4 (NEURL4) mediates ADP-ribosylation of mitochondrial proteins. J Cell Biol 2022; 221:213006. [PMID: 35157000 PMCID: PMC8932523 DOI: 10.1083/jcb.202101021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/07/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
ADP-ribosylation is a reversible post-translational modification where an ADP-ribose moiety is covalently attached to target proteins by ADP-ribosyltransferases (ARTs). Although best known for its nuclear roles, ADP-ribosylation is increasingly recognized as a key regulatory strategy across cellular compartments. ADP-ribosylation of mitochondrial proteins has been widely reported, but the exact nature of mitochondrial ART enzymes is debated. We have identified neuralized-like protein 4 (NEURL4) as a mitochondrial ART enzyme and show that most ART activity associated with mitochondria is lost in the absence of NEURL4. The NEURL4-dependent ADP-ribosylome in mitochondrial extracts from HeLa cells includes numerous mitochondrial proteins previously shown to be ADP-ribosylated. In particular, we show that NEURL4 is required for the regulation of mtDNA integrity via poly-ADP-ribosylation of mtLIG3, the rate-limiting enzyme for base excision repair (BER). Collectively, our studies reveal that NEURL4 acts as the main mitochondrial ART enzyme under physiological conditions and provide novel insights in the regulation of mitochondria homeostasis through ADP-ribosylation.
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Affiliation(s)
| | - Yuan Gao
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Julian Kwan
- Department of Biochemistry, Boston University School of Medicine, Boston, MA.,Center for Network Systems Biology, Boston University, Boston, MA
| | - Vanessa Hayashi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Megan Sheeran
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Junxiang Xu
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Justin English
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Joseph Orofino
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Andrew Emili
- Department of Biochemistry, Boston University School of Medicine, Boston, MA.,Center for Network Systems Biology, Boston University, Boston, MA
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
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99
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Sowa ST, Lehtiö L. The zinc-binding motif in tankyrases is required for the structural integrity of the catalytic ADP-ribosyltransferase domain. Open Biol 2022; 12:210365. [PMID: 35317661 PMCID: PMC8941426 DOI: 10.1098/rsob.210365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Tankyrases are ADP-ribosylating enzymes that regulate many physiological processes in the cell and are considered promising drug targets for cancer and fibrotic diseases. The catalytic ADP-ribosyltransferase domain of tankyrases contains a unique zinc-binding motif of unknown function. Recently, this motif was suggested to be involved in the catalytic activity of tankyrases. In this work, we set out to study the effect of the zinc-binding motif on the activity, stability and structure of human tankyrases. We generated mutants of human tankyrase (TNKS) 1 and TNKS2, abolishing the zinc-binding capabilities, and characterized the proteins biochemically and biophysically in vitro. We further generated a crystal structure of TNKS2, in which the zinc ion was oxidatively removed. Our work shows that the zinc-binding motif in tankyrases is a crucial structural element which is particularly important for the structural integrity of the acceptor site. While mutation of the motif rendered TNKS1 inactive, probably due to introduction of major structural defects, the TNKS2 mutant remained active and displayed an altered activity profile compared to the wild-type.
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Affiliation(s)
- Sven T. Sowa
- Faculty for Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lari Lehtiö
- Faculty for Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
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Toward More Comprehensive Homologous Recombination Deficiency Assays in Ovarian Cancer, Part 1: Technical Considerations. Cancers (Basel) 2022; 14:cancers14051132. [PMID: 35267439 PMCID: PMC8909526 DOI: 10.3390/cancers14051132] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary High-grade serous ovarian cancer (HGSOC) is the most frequent and lethal form of ovarian cancer and is associated with homologous recombination deficiency (HRD) in 50% of cases. This specific alteration is associated with sensitivity to PARP inhibitors (PARPis). Despite vast prognostic improvements due to PARPis, current molecular assays assessing HRD status suffer from several limitations, and there is an urgent need for a more accurate evaluation. In these companion reviews (Part 1: Technical considerations; Part 2: Medical perspectives), we develop an integrative review to provide physicians and researchers involved in HGSOC management with a holistic perspective, from translational research to clinical applications. Abstract High-grade serous ovarian cancer (HGSOC), the most frequent and lethal form of ovarian cancer, exhibits homologous recombination deficiency (HRD) in 50% of cases. In addition to mutations in BRCA1 and BRCA2, which are the best known thus far, defects can also be caused by diverse alterations to homologous recombination-related genes or epigenetic patterns. HRD leads to genomic instability (genomic scars) and is associated with PARP inhibitor (PARPi) sensitivity. HRD is currently assessed through BRCA1/2 analysis, which produces a genomic instability score (GIS). However, despite substantial clinical achievements, FDA-approved companion diagnostics (CDx) based on GISs have important limitations. Indeed, despite the use of GIS in clinical practice, the relevance of such assays remains controversial. Although international guidelines include companion diagnostics as part of HGSOC frontline management, they also underscore the need for more powerful and alternative approaches for assessing patient eligibility to PARP inhibitors. In these companion reviews, we review and present evidence to date regarding HRD definitions, achievements and limitations in HGSOC. Part 1 is dedicated to technical considerations and proposed perspectives that could lead to a more comprehensive and dynamic assessment of HR, while Part 2 provides a more integrated approach for clinicians.
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